Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionQ46802
DateWed Jan 25 15:21:12 GMT 2012
Unique Job ID82810ccb12125ae1

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1ny5A_
Top template information
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state
Confidence and coverage
Confidence:100.0% Coverage: 45%
269 residues ( 45% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
574 residues ( 97%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MELATTQSVLMQIQPTIQRFARMLASVLQLEVEIVDENLCRVAGTGAYGKFLGRQLSGNS
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Disorder  ?????






















































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   .........70.........80.........90.........100.........110.........120
Sequence  RLLRHVLETKTEKVVTQSRFDPLCEGCDSKENCREKAFLGTPVILQDRCVGVISLIAVTH
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?






































?
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   .........130.........140.........150.........160.........170.........180
Sequence  EQQEHISDNLREFSDYVRHISTIFVSKLLEDQGPGDNISKIFATMIDNMDQGVLVVDDEN
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   .........190.........200.........210.........220.........230.........240
Sequence  RVQFVNQTALKTLGVVQNNIIGKPIRFRPLTFESNFTHGHMQHIVSWDDKSELIIGQLHN
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?????????








???







?
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   .........250.........260.........270.........280.........290.........300
Sequence  IQGRQLFLMAFHQSHTSFSVANAPDEPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVG
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???????????????

























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   .........310.........320.........330.........340.........350.........360
Sequence  ESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGL
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???????





























??????
?
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   .........370.........380.........390.........400.........410.........420
Sequence  IQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQF
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   .........430.........440.........450.........460.........470.........480
Sequence  IAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEI
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???







































?

??
?







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   .........490.........500.........510.........520.........530.........540
Sequence  LRKHRWPGNLRELSNLMEYLVNVVPSGEVIDSTLLPPNLLNNGTTEQSDVTEVSEAHLSL
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?








????????????????????
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   .........550.........560.........570.........580.........590..
Sequence  DDAGGTALEEMEKQMIREALSRHNSKKQVADELGIGIATLYRKIKKYELLNT
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??????
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Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 1ny5 chain A

3D model

Region: 249 - 519
Aligned: 269
Modelled: 271
Confidence: 100.0%
Identity: 43%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state

Phyre2

PDB 3dzd chain A

3D model

Region: 239 - 512
Aligned: 271
Modelled: 274
Confidence: 100.0%
Identity: 45%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4 in the inactive2 state

Phyre2

PDB 2c99 chain A

3D model

Region: 272 - 516
Aligned: 236
Modelled: 245
Confidence: 100.0%
Identity: 42%
PDB header:transcription regulation
Chain: A: PDB Molecule:psp operon transcriptional activator;
PDBTitle: structural basis of the nucleotide driven conformational2 changes in the aaa domain of transcription activator pspf

Phyre2

PDB 1ny5 chain A domain 2

3D model

Region: 271 - 519
Aligned: 247
Modelled: 249
Confidence: 100.0%
Identity: 47%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1ojl chain F

3D model

Region: 271 - 521
Aligned: 246
Modelled: 251
Confidence: 100.0%
Identity: 46%
PDB header:response regulator
Chain: F: PDB Molecule:transcriptional regulatory protein zrar;
PDBTitle: crystal structure of a sigma54-activator suggests the2 mechanism for the conformational switch necessary for3 sigma54 binding

Phyre2

PDB 3co5 chain B

3D model

Region: 275 - 444
Aligned: 132
Modelled: 146
Confidence: 100.0%
Identity: 25%
PDB header:transcription regulator
Chain: B: PDB Molecule:putative two-component system transcriptional response
PDBTitle: crystal structure of sigma-54 interaction domain of putative2 transcriptional response regulator from neisseria gonorrhoeae

Phyre2

PDB 3pfi chain B

3D model

Region: 267 - 587
Aligned: 253
Modelled: 286
Confidence: 99.9%
Identity: 15%
PDB header:hydrolase
Chain: B: PDB Molecule:holliday junction atp-dependent dna helicase ruvb;
PDBTitle: 2.7 angstrom resolution crystal structure of a probable holliday2 junction dna helicase (ruvb) from campylobacter jejuni subsp. jejuni3 nctc 11168 in complex with adenosine-5'-diphosphate

Phyre2

PDB 1r6b chain X domain 3

3D model

Region: 270 - 501
Aligned: 228
Modelled: 232
Confidence: 99.9%
Identity: 15%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1r6b chain X

3D model

Region: 270 - 501
Aligned: 226
Modelled: 232
Confidence: 99.8%
Identity: 17%
PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa

Phyre2

PDB 1qvr chain B

3D model

Region: 270 - 501
Aligned: 215
Modelled: 218
Confidence: 99.8%
Identity: 19%
PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb

Phyre2

PDB 1um8 chain A

3D model

Region: 270 - 501
Aligned: 217
Modelled: 232
Confidence: 99.8%
Identity: 18%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3pxi chain B

3D model

Region: 269 - 501
Aligned: 211
Modelled: 216
Confidence: 99.8%
Identity: 17%
PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc

Phyre2

PDB 1in8 chain A

3D model

Region: 265 - 587
Aligned: 257
Modelled: 277
Confidence: 99.8%
Identity: 18%
PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v

Phyre2

PDB 3nbx chain X

3D model

Region: 280 - 513
Aligned: 212
Modelled: 229
Confidence: 99.8%
Identity: 19%
PDB header:hydrolase
Chain: X: PDB Molecule:atpase rava;
PDBTitle: crystal structure of e. coli rava (regulatory atpase variant a) in2 complex with adp

Phyre2

PDB 1qvr chain A domain 3

3D model

Region: 270 - 501
Aligned: 217
Modelled: 232
Confidence: 99.8%
Identity: 17%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3pvs chain A

3D model

Region: 265 - 570
Aligned: 238
Modelled: 270
Confidence: 99.8%
Identity: 24%
PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa

Phyre2

PDB 3k1j chain A

3D model

Region: 269 - 520
Aligned: 243
Modelled: 252
Confidence: 99.8%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent protease lon;
PDBTitle: crystal structure of lon protease from thermococcus onnurineus na1

Phyre2

PDB 1l8q chain A domain 2

3D model

Region: 266 - 502
Aligned: 202
Modelled: 237
Confidence: 99.7%
Identity: 15%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3f8t chain A

3D model

Region: 291 - 520
Aligned: 210
Modelled: 230
Confidence: 99.7%
Identity: 13%
PDB header:hydrolase
Chain: A: PDB Molecule:predicted atpase involved in replication control,
PDBTitle: crystal structure analysis of a full-length mcm homolog2 from methanopyrus kandleri

Phyre2

PDB 2hcb chain C

3D model

Region: 265 - 500
Aligned: 201
Modelled: 236
Confidence: 99.7%
Identity: 15%
PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus

Phyre2

PDB 1ntc chain A

3D model

Region: 485 - 590
Aligned: 89
Modelled: 89
Confidence: 99.5%
Identity: 28%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2

PDB 2w1r chain A

3D model

Region: 15 - 137
Aligned: 116
Modelled: 116
Confidence: 99.1%
Identity: 14%
PDB header:transcription
Chain: A: PDB Molecule:stage v sporulation protein t;
PDBTitle: crystal structure of the c-terminal domain of b. subtilis2 spovt

Phyre2

PDB 3p01 chain C

3D model

Region: 12 - 147
Aligned: 134
Modelled: 132
Confidence: 98.9%
Identity: 11%
PDB header:signaling protein
Chain: C: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120

Phyre2

PDB 3mmh chain A

3D model

Region: 12 - 149
Aligned: 132
Modelled: 132
Confidence: 98.9%
Identity: 14%
PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase;
PDBTitle: x-ray structure of free methionine-r-sulfoxide reductase from2 neisseria meningitidis in complex with its substrate

Phyre2

PDB 3o5y chain A

3D model

Region: 12 - 146
Aligned: 133
Modelled: 132
Confidence: 98.9%
Identity: 13%
PDB header:transcription regulator
Chain: A: PDB Molecule:sensor protein;
PDBTitle: the crystal structure of the gaf domain of a two-component sensor2 histidine kinase from bacillus halodurans to 2.45a

Phyre2

PDB 3ksi chain A

3D model

Region: 12 - 145
Aligned: 126
Modelled: 126
Confidence: 98.9%
Identity: 11%
PDB header:oxidoreductase
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: structure of frmsr of staphylococcus aureus (complex with 2-propanol)

Phyre2

PDB 3p01 chain A

3D model

Region: 12 - 148
Aligned: 135
Modelled: 133
Confidence: 98.8%
Identity: 11%
PDB header:signaling protein
Chain: A: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120

Phyre2

PDB 3ibj chain B

3D model

Region: 12 - 183
Aligned: 170
Modelled: 170
Confidence: 98.7%
Identity: 16%
PDB header:hydrolase
Chain: B: PDB Molecule:cgmp-dependent 3',5'-cyclic phosphodiesterase;
PDBTitle: x-ray structure of pde2a

Phyre2

PDB 2wkq chain A

3D model

Region: 166 - 313
Aligned: 126
Modelled: 126
Confidence: 98.6%
Identity: 17%
PDB header:transferase, cell adhesion
Chain: A: PDB Molecule:nph1-1, ras-related c3 botulinum toxin substrate
PDBTitle: structure of a photoactivatable rac1 containing the lov22 c450a mutant

Phyre2

PDB 3mfx chain A

3D model

Region: 156 - 235
Aligned: 80
Modelled: 79
Confidence: 98.5%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:sensory box/ggdef family protein;
PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b

Phyre2

PDB 2jhe chain B

3D model

Region: 154 - 239
Aligned: 86
Modelled: 86
Confidence: 98.4%
Identity: 14%
PDB header:transcription
Chain: B: PDB Molecule:transcription regulator tyrr;
PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190)

Phyre2

PDB 3b33 chain A

3D model

Region: 161 - 242
Aligned: 82
Modelled: 80
Confidence: 98.3%
Identity: 12%
PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus

Phyre2

PDB 3olo chain B

3D model

Region: 156 - 213
Aligned: 58
Modelled: 56
Confidence: 98.3%
Identity: 12%
PDB header:transferase
Chain: B: PDB Molecule:two-component sensor histidine kinase;
PDBTitle: crystal structure of a pas domain from two-component sensor histidine2 kinase

Phyre2

PDB 1nwz chain A

3D model

Region: 150 - 215
Aligned: 66
Modelled: 66
Confidence: 98.2%
Identity: 14%
Fold: Profilin-like
Superfamily: PYP-like sensor domain (PAS domain)
Family: PYP-like

Phyre2
1

c1ny5A_
2

c3dzdA_
3

c2c99A_
4

d1ny5a2
5

c1ojlF_
6

c3co5B_
7

c3pfiB_
8

d1r6bx3
9

c1r6bX_
10

c1qvrB_
11

d1um8a_
12

c3pxiB_
13

c1in8A_
14

c3nbxX_
15

d1qvra3
16

c3pvsA_
17

c3k1jA_
18

d1l8qa2
19

c3f8tA_
20

c2hcbC_
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d1ntca_
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c2w1rA_
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c3p01C_
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c3mmhA_
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c3o5yA_
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c3ksiA_
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c3p01A_
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c3ibjB_
102

c2wkqA_
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c3mfxA_
115



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c2jheB_
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c3b33A_
128

c3oloB_
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d1nwza_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1ny5A_



100.0 43 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state
2c3dzdA_



100.0 45 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4 in the inactive2 state
3c2c99A_



100.0 42 PDB header:transcription regulation
Chain: A: PDB Molecule:psp operon transcriptional activator;
PDBTitle: structural basis of the nucleotide driven conformational2 changes in the aaa domain of transcription activator pspf
4d1ny5a2



100.0 47 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
5c1ojlF_



100.0 46 PDB header:response regulator
Chain: F: PDB Molecule:transcriptional regulatory protein zrar;
PDBTitle: crystal structure of a sigma54-activator suggests the2 mechanism for the conformational switch necessary for3 sigma54 binding
6c3co5B_



100.0 25 PDB header:transcription regulator
Chain: B: PDB Molecule:putative two-component system transcriptional response
PDBTitle: crystal structure of sigma-54 interaction domain of putative2 transcriptional response regulator from neisseria gonorrhoeae
7c3pfiB_



99.9 15 PDB header:hydrolase
Chain: B: PDB Molecule:holliday junction atp-dependent dna helicase ruvb;
PDBTitle: 2.7 angstrom resolution crystal structure of a probable holliday2 junction dna helicase (ruvb) from campylobacter jejuni subsp. jejuni3 nctc 11168 in complex with adenosine-5'-diphosphate
8d1r6bx3



99.9 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
9c1r6bX_



99.8 17 PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa
10c1qvrB_



99.8 19 PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb
11d1um8a_



99.8 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
12c3pxiB_



99.8 17 PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc
13c1in8A_



99.8 18 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
14c3nbxX_



99.8 19 PDB header:hydrolase
Chain: X: PDB Molecule:atpase rava;
PDBTitle: crystal structure of e. coli rava (regulatory atpase variant a) in2 complex with adp
15d1qvra3



99.8 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
16c3pvsA_



99.8 24 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
17c3k1jA_



99.8 24 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent protease lon;
PDBTitle: crystal structure of lon protease from thermococcus onnurineus na1
18d1l8qa2



99.7 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
19c3f8tA_



99.7 13 PDB header:hydrolase
Chain: A: PDB Molecule:predicted atpase involved in replication control,
PDBTitle: crystal structure analysis of a full-length mcm homolog2 from methanopyrus kandleri
20c2hcbC_



99.7 15 PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus
21c1nsfA_



not modelled 99.6 19 PDB header:protein transport
Chain: A: PDB Molecule:n-ethylmaleimide sensitive factor;
PDBTitle: d2 hexamerization domain of n-ethylmaleimide sensitive factor (nsf)
22d1g41a_



not modelled 99.6 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
23d1g8pa_



not modelled 99.6 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
24c2r44A_



not modelled 99.6 13 PDB header:hydrolase
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a putative atpase (chu_0153) from cytophaga2 hutchinsonii atcc 33406 at 2.00 a resolution
25c3bosA_



not modelled 99.6 14 PDB header:hydrolase regulator,dna binding protein
Chain: A: PDB Molecule:putative dna replication factor;
PDBTitle: crystal structure of a putative dna replication regulator hda2 (sama_1916) from shewanella amazonensis sb2b at 1.75 a resolution
26c2z4rB_



not modelled 99.6 12 PDB header:dna binding protein
Chain: B: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: crystal structure of domain iii from the thermotoga2 maritima replication initiation protein dnaa
27c3hteC_



not modelled 99.6 17 PDB header:motor protein
Chain: C: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: crystal structure of nucleotide-free hexameric clpx
28c1hqcB_



not modelled 99.6 18 PDB header:hydrolase
Chain: B: PDB Molecule:ruvb;
PDBTitle: structure of ruvb from thermus thermophilus hb8
29c2c9oC_



not modelled 99.5 19 PDB header:hydrolase
Chain: C: PDB Molecule:ruvb-like 1;
PDBTitle: 3d structure of the human ruvb-like helicase ruvbl1
30c3f9vA_



not modelled 99.5 14 PDB header:hydrolase
Chain: A: PDB Molecule:minichromosome maintenance protein mcm;
PDBTitle: crystal structure of a near full-length archaeal mcm: functional2 insights for an aaa+ hexameric helicase
31d1ofha_



not modelled 99.5 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
32d1in4a2



not modelled 99.5 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
33d1ixsb2



not modelled 99.5 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
34d1ntca_



99.5 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
35d1fnna2



not modelled 99.5 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
36d1sxjd2



not modelled 99.4 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
37d1d2na_



not modelled 99.4 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
38d1etob_



not modelled 99.4 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
39d1iqpa2



not modelled 99.3 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
40d1fipa_



not modelled 99.3 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
41c2chgB_



not modelled 99.3 23 PDB header:dna-binding protein
Chain: B: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c domains 1 and 2
42d1njfa_



not modelled 99.3 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
43d1g2ha_



not modelled 99.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
44c2dhrC_



not modelled 99.3 21 PDB header:hydrolase
Chain: C: PDB Molecule:ftsh;
PDBTitle: whole cytosolic region of atp-dependent metalloprotease2 ftsh (g399l)
45c3b9pA_



not modelled 99.3 21 PDB header:hydrolase
Chain: A: PDB Molecule:cg5977-pa, isoform a;
PDBTitle: spastin
46d1etxa_



not modelled 99.3 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
47c2ce7B_



not modelled 99.2 24 PDB header:cell division protein
Chain: B: PDB Molecule:cell division protein ftsh;
PDBTitle: edta treated
48d1sxjb2



not modelled 99.2 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
49d1umqa_



not modelled 99.2 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
50c1umqA_



not modelled 99.2 15 PDB header:dna-binding protein
Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein;
PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
51c3eihB_



not modelled 99.2 19 PDB header:protein transport
Chain: B: PDB Molecule:vacuolar protein sorting-associated protein 4;
PDBTitle: crystal structure of s.cerevisiae vps4 in the presence of atpgammas
52c3e7lD_



not modelled 99.2 33 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
53c2kjqA_



not modelled 99.2 23 PDB header:replication
Chain: A: PDB Molecule:dnaa-related protein;
PDBTitle: solution structure of protein nmb1076 from neisseria meningitidis.2 northeast structural genomics consortium target mr101b.
54d1sxjc2



not modelled 99.2 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
55c3h4mC_



not modelled 99.2 16 PDB header:hydrolase
Chain: C: PDB Molecule:proteasome-activating nucleotidase;
PDBTitle: aaa atpase domain of the proteasome- activating nucleotidase
56d1w5sa2



not modelled 99.1 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
57c2w1rA_



99.1 14 PDB header:transcription
Chain: A: PDB Molecule:stage v sporulation protein t;
PDBTitle: crystal structure of the c-terminal domain of b. subtilis2 spovt
58c2p65A_



not modelled 99.1 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pf08_0063;
PDBTitle: crystal structure of the first nucleotide binding domain of2 chaperone clpb1, putative, (pv089580) from plasmodium vivax
59d1qvra2



not modelled 99.1 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
60c1xxhB_



not modelled 99.1 20 PDB header:transferase
Chain: B: PDB Molecule:dna polymerase iii subunit gamma;
PDBTitle: atpgs bound e. coli clamp loader complex
61d2ce7a2



not modelled 99.1 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
62c1xwiA_



not modelled 99.1 19 PDB header:protein transport
Chain: A: PDB Molecule:skd1 protein;
PDBTitle: crystal structure of vps4b
63c3d8bB_



not modelled 99.1 17 PDB header:hydrolase
Chain: B: PDB Molecule:fidgetin-like protein 1;
PDBTitle: crystal structure of human fidgetin-like protein 1 in complex with adp
64c1sxjD_



not modelled 99.1 15 PDB header:replication
Chain: D: PDB Molecule:activator 1 41 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
65c3u5zM_



not modelled 99.1 19 PDB header:dna binding protein/dna
Chain: M: PDB Molecule:dna polymerase accessory protein 44;
PDBTitle: structure of t4 bacteriophage clamp loader bound to the t4 clamp,2 primer-template dna, and atp analog
66c2r65A_



not modelled 99.0 16 PDB header:hydrolase
Chain: A: PDB Molecule:cell division protease ftsh homolog;
PDBTitle: crystal structure of helicobacter pylori atp dependent protease, ftsh2 adp complex
67c1fnnB_



not modelled 99.0 11 PDB header:cell cycle
Chain: B: PDB Molecule:cell division control protein 6;
PDBTitle: crystal structure of cdc6p from pyrobaculum aerophilum
68d1r6bx2



not modelled 99.0 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
69c1sxjB_



not modelled 99.0 19 PDB header:replication
Chain: B: PDB Molecule:activator 1 37 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
70d1lv7a_



not modelled 99.0 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
71c2qbyB_



not modelled 99.0 16 PDB header:replication/dna
Chain: B: PDB Molecule:cell division control protein 6 homolog 3;
PDBTitle: crystal structure of a heterodimer of cdc6/orc1 initiators2 bound to origin dna (from s. solfataricus)
72c2v1uA_



not modelled 99.0 17 PDB header:replication
Chain: A: PDB Molecule:cell division control protein 6 homolog;
PDBTitle: structure of the aeropyrum pernix orc1 protein in complex2 with dna
73c3cf1C_



not modelled 99.0 22 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
74c2qbyA_



not modelled 99.0 15 PDB header:replication/dna
Chain: A: PDB Molecule:cell division control protein 6 homolog 1;
PDBTitle: crystal structure of a heterodimer of cdc6/orc1 initiators2 bound to origin dna (from s. solfataricus)
75d1sxja2



not modelled 99.0 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
76c1iy2A_



not modelled 98.9 22 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent metalloprotease ftsh;
PDBTitle: crystal structure of the ftsh atpase domain from thermus2 thermophilus
77c3p01C_



98.9 11 PDB header:signaling protein
Chain: C: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120
78c3mmhA_



98.9 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase;
PDBTitle: x-ray structure of free methionine-r-sulfoxide reductase from2 neisseria meningitidis in complex with its substrate
79c1sxjC_



not modelled 98.9 16 PDB header:replication
Chain: C: PDB Molecule:activator 1 40 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
80c3o5yA_



98.9 13 PDB header:transcription regulator
Chain: A: PDB Molecule:sensor protein;
PDBTitle: the crystal structure of the gaf domain of a two-component sensor2 histidine kinase from bacillus halodurans to 2.45a
81c2qz4A_



not modelled 98.9 16 PDB header:hydrolase
Chain: A: PDB Molecule:paraplegin;
PDBTitle: human paraplegin, aaa domain in complex with adp
82d1ixza_



not modelled 98.9 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
83c2chvE_



not modelled 98.9 23 PDB header:dna-binding protein
Chain: E: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c adpnp complex
84c3ksiA_



98.9 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: structure of frmsr of staphylococcus aureus (complex with 2-propanol)
85d1sxje2



not modelled 98.9 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
86c2zamA_



not modelled 98.9 23 PDB header:protein transport
Chain: A: PDB Molecule:vacuolar protein sorting-associating protein 4b;
PDBTitle: crystal structure of mouse skd1/vps4b apo-form
87d1e32a2



not modelled 98.9 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
88c3hu2C_



not modelled 98.9 23 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
89c1iqpF_



not modelled 98.9 22 PDB header:replication
Chain: F: PDB Molecule:rfcs;
PDBTitle: crystal structure of the clamp loader small subunit from2 pyrococcus furiosus
90c2x8aA_



not modelled 98.8 12 PDB header:nuclear protein
Chain: A: PDB Molecule:nuclear valosin-containing protein-like;
PDBTitle: human nuclear valosin containing protein like (nvl), c-2 terminal aaa-atpase domain
91c3trcA_



not modelled 98.8 12 PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of the gaf domain from a phosphoenolpyruvate-protein2 phosphotransferase (ptsp) from coxiella burnetii
92c3p01A_



98.8 11 PDB header:signaling protein
Chain: A: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120
93d1vhma_



not modelled 98.8 7 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
94c1sxjA_



not modelled 98.8 15 PDB header:replication
Chain: A: PDB Molecule:activator 1 95 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
95c1vhmB_



not modelled 98.8 7 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:protein yebr;
PDBTitle: crystal structure of an hypothetical protein
96d1jbka_



not modelled 98.8 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
97c3eeaB_



not modelled 98.8 16 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:gaf domain/hd domain protein;
PDBTitle: the crystal structure of the gaf domain/hd domain protein2 from geobacter sulfurreducens
98d1e94e_



not modelled 98.7 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
99c1sxjE_



not modelled 98.7 19 PDB header:replication
Chain: E: PDB Molecule:activator 1 40 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
100c1mc0A_



not modelled 98.7 14 PDB header:hydrolase
Chain: A: PDB Molecule:3',5'-cyclic nucleotide phosphodiesterase 2a;
PDBTitle: regulatory segment of mouse 3',5'-cyclic nucleotide phosphodiesterase2 2a, containing the gaf a and gaf b domains
101c3ibjB_



98.7 16 PDB header:hydrolase
Chain: B: PDB Molecule:cgmp-dependent 3',5'-cyclic phosphodiesterase;
PDBTitle: x-ray structure of pde2a
102c2wkqA_



98.6 17 PDB header:transferase, cell adhesion
Chain: A: PDB Molecule:nph1-1, ras-related c3 botulinum toxin substrate
PDBTitle: structure of a photoactivatable rac1 containing the lov22 c450a mutant
103d2veaa1



not modelled 98.6 10 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
104d1f5ma_



not modelled 98.6 14 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
105c3mf0A_



not modelled 98.6 14 PDB header:hydrolase
Chain: A: PDB Molecule:cgmp-specific 3',5'-cyclic phosphodiesterase;
PDBTitle: crystal structure of pde5a gaf domain (89-518)
106c1s3sA_



not modelled 98.6 20 PDB header:protein binding
Chain: A: PDB Molecule:transitional endoplasmic reticulum atpase (ter
PDBTitle: crystal structure of aaa atpase p97/vcp nd1 in complex with2 p47 c
107d1r7ra3



not modelled 98.6 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
108c3dbaB_



not modelled 98.6 11 PDB header:hydrolase
Chain: B: PDB Molecule:cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit
PDBTitle: crystal structure of the cgmp-bound gaf a domain from the2 photoreceptor phosphodiesterase 6c
109d2o9ca1



not modelled 98.5 11 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
110c3hcyB_



not modelled 98.5 10 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative two-component sensor histidine kinase protein;
PDBTitle: the crystal structure of the domain of putative two-component sensor2 histidine kinase protein from sinorhizobium meliloti 1021
111c3ec2A_



not modelled 98.5 17 PDB header:replication
Chain: A: PDB Molecule:dna replication protein dnac;
PDBTitle: crystal structure of the dnac helicase loader
112c2vjwA_



not modelled 98.5 9 PDB header:hydrolase
Chain: A: PDB Molecule:gaf family protein;
PDBTitle: crystal structure of the second gaf domain of devs from2 mycobacterium smegmatis
113c1jr3E_



not modelled 98.5 15 PDB header:transferase
Chain: E: PDB Molecule:dna polymerase iii, delta' subunit;
PDBTitle: crystal structure of the processivity clamp loader gamma2 complex of e. coli dna polymerase iii
114c3mfxA_



98.5 13 PDB header:transcription
Chain: A: PDB Molecule:sensory box/ggdef family protein;
PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b
115c3ci6B_



not modelled 98.5 11 PDB header:transferase
Chain: B: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: crystal structure of the gaf domain from acinetobacter2 phosphoenolpyruvate-protein phosphotransferase
116c2qybA_



not modelled 98.4 12 PDB header:membrane protein
Chain: A: PDB Molecule:membrane protein, putative;
PDBTitle: crystal structure of the gaf domain region of putative membrane2 protein from geobacter sulfurreducens pca
117c2jheB_



98.4 14 PDB header:transcription
Chain: B: PDB Molecule:transcription regulator tyrr;
PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190)
118c3oovA_



not modelled 98.4 13 PDB header:signaling protein
Chain: A: PDB Molecule:methyl-accepting chemotaxis protein, putative;
PDBTitle: crystal structure of a methyl-accepting chemotaxis protein, residues2 122 to 287
119c3pxgA_



not modelled 98.4 20 PDB header:protein binding
Chain: A: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca121 and clpc1-485 complex
120c2w3gA_



not modelled 98.4 15 PDB header:transferase
Chain: A: PDB Molecule:two component sensor histidine kinase devs (gaf
PDBTitle: air-oxidized structure of the first gaf domain of2 mycobacterium tuberculosis doss

Binding site prediction 

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite



Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0